高度异源-同源多倍体的现代甘蔗基因组以及甘蔗中非常近期的异源多倍体化。

The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum.

作者信息

Zhang Jisen, Qi Yiying, Hua Xiuting, Wang Yongjun, Wang Baiyu, Qi Yongwen, Huang Yumin, Yu Zehuai, Gao Ruiting, Zhang Yixing, Wang Tianyou, Wang Yuhao, Mei Jing, Zhang Qing, Wang Gang, Pan Haoran, Li Zhen, Li Shuangyu, Liu Jia, Qi Nameng, Feng Xiaoxi, Wu Mingxing, Chen Shuqi, Du Cuicui, Li Yihan, Xu Yi, Fang Yaxue, Ma Panpan, Li Qingyun, Sun Yuanchang, Feng Xiaomin, Yao Wei, Zhang Muqing, Chen Baoshan, Liu Xinlong, Ming Ray, Wang Jianping, Deng Zuhu, Tang Haibao

机构信息

State Key Lab for Conservation and Utilization of Subtropical Agro-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China.

College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.

出版信息

Nat Genet. 2025 Jan;57(1):242-253. doi: 10.1038/s41588-024-02033-w. Epub 2025 Jan 3.

DOI:10.1038/s41588-024-02033-w

PMID:39753769

Abstract

Modern sugarcane, a highly allo-autopolyploid organism, has a very complex genome. In the present study, the karyotype and genome architecture of modern sugarcane were investigated, resulting in a genome assembly of 97 chromosomes (8.84 Gb). The allopolyploid genome was divided into subgenomes from Saccharum officinarum (So) and S. spontaneum (Ss), with So dominance in the Saccharum hybrid (S. hybrid). Genome shock affected transcriptome dynamics during allopolyploidization. Analysis of an inbreeding population with 192 individuals revealed the underlying genetic basis of transgressive segregation. Population genomics of 310 Saccharum accessions clarified the breeding history of modern sugarcane. Using the haplotype-resolved S. hybrid genome as a reference, genome-wide association studies identified a potential candidate gene for sugar content from S. spontaneum. These findings illuminate the complex genome evolution of allopolyploids, offering opportunities for genomic enhancements and innovative breeding strategies for sugarcane.

摘要

现代甘蔗是一种高度异源-同源多倍体生物，具有非常复杂的基因组。在本研究中，对现代甘蔗的核型和基因组结构进行了研究，得到了一个由97条染色体（8.84 Gb）组成的基因组组装。异源多倍体基因组被分为源自甘蔗（So）和野生甘蔗（Ss）的亚基因组，在甘蔗杂交种（S. hybrid）中So占主导地位。基因组冲击影响了异源多倍体化过程中的转录组动态。对一个由192个个体组成的近交群体的分析揭示了超亲分离的潜在遗传基础。对310份甘蔗种质的群体基因组学研究阐明了现代甘蔗的育种历史。以单倍型解析的S. hybrid基因组为参考，全基因组关联研究确定了一个来自野生甘蔗的潜在含糖量候选基因。这些发现阐明了异源多倍体复杂的基因组进化，为甘蔗的基因组改良和创新育种策略提供了机会。